First, download Nvidia Profile Inspector from https://ci.appveyor.com/project/Orbmu2k/nvidiaprofileinspector/build/artifacts
Second, download the Agony Unofficial SLI Patch from https://drive.google.com/open?id=1u8_TwTFB9a4LhncINHnQXNtZaZkOxYHJ
Launch Nvidia Profile Inspector, and at the top, select import and import the Agony profile.

When in game, set Anti Aliasing to Medium or Low. High and Ultra uses Temporal AA, which causes SLI to not scale.
To get rid of the shimmering caused by Post Processing, set Post Processing to Medium or Low.

If you wish to recreate the fix manually, launch Nvidia Profile Inspector, click on the star at the top to create a profile for Agony, add the Agony-Win64-Shipping executible located in ...steamapps\common\Agony\Agony\Binaries\Win64, and select the magnifying glass labeled Show Unknown Settings at the top. From there, mirror the settings listed in black from here https://i.imgur.com/Bp4JD2b.png

Proof SLI works.

SLI disabled
https://i.imgur.com/5cyzSUw.jpg
https://i.imgur.com/TCRqa3h.jpg

SLI enabled
https://i.imgur.com/mhUAbLW.jpg
https://i.imgur.com/z9AwXrw.jpg